4917 refactor nicknaming hapi with version bump (#4955)

* refactoring 1 * refactoring step 2 * refactoring matches * cleanup * fixing some tests * fixing more tests * remove dbugcode * adding the nickname factory * code review fixes * review fixes * put default to prevent breaking * refactor review fixes * more review points * more review points * review points * review points * more review changes * review points * review points * adding bean * updating version --------- Co-authored-by: leif stawnyczy <[email protected]> Co-authored-by: leif stawnyczy <[email protected]>
hapifhir · Jun 6, 2023 · 0a7f97a · 0a7f97a
1 parent 6c03a51
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diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-android/pom.xml b/hapi-fhir-android/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-base/pom.xml b/hapi-fhir-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-bom/pom.xml b/hapi-fhir-bom/pom.xml
@@ -4,15 +4,15 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-bom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <packaging>pom</packaging>
  <name>HAPI FHIR BOM</name>
 
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-checkstyle/pom.xml b/hapi-fhir-checkstyle/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
@@ -6,7 +6,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-cli</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-cli/pom.xml b/hapi-fhir-cli/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-client-okhttp/pom.xml b/hapi-fhir-client-okhttp/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-client/pom.xml b/hapi-fhir-client/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-converter/pom.xml b/hapi-fhir-converter/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-dist/pom.xml b/hapi-fhir-dist/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-docs/pom.xml b/hapi-fhir-docs/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/...r-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4917-refactoring-matchers.yaml b/...r-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/4917-refactoring-matchers.yaml
@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 4917
+title: "Matching algorithms have been refactored to allow
+ greater flexibility in setting and defining nicknames
+ as well as allowing bean injection into matcher classes.
+ "
diff --git a/hapi-fhir-jacoco/pom.xml b/hapi-fhir-jacoco/pom.xml
@@ -11,7 +11,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jaxrsserver-base/pom.xml b/hapi-fhir-jaxrsserver-base/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpa/pom.xml b/hapi-fhir-jpa/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/...jpa/searchparam/nickname/NicknameMap.java → ...ca/uhn/fhir/jpa/nickname/NicknameMap.java b/...jpa/searchparam/nickname/NicknameMap.java → ...ca/uhn/fhir/jpa/nickname/NicknameMap.java
@@ -17,7 +17,7 @@
  * limitations under the License.
  * #L%
  */
-package ca.uhn.fhir.jpa.searchparam.nickname;
+package ca.uhn.fhir.jpa.nickname;
 
 import javax.annotation.Nonnull;
 import java.io.BufferedReader;
@@ -33,19 +33,30 @@ class NicknameMap {
  private final Map<String, List<String>> myFormalToNick = new HashMap<>();
  private final Map<String, List<String>> myNicknameToFormal = new HashMap<>();
 
+ private final List<String> myBadRows = new ArrayList<>();
+
  void load(Reader theReader) throws IOException {
  try (BufferedReader reader = new BufferedReader(theReader)) {
  String line;
  while ((line = reader.readLine()) != null) {
  String[] parts = line.split(",");
- String key = parts[0];
- List<String> values = new ArrayList<>(Arrays.asList(parts).subList(1, parts.length));
- add(key, values);
+ if (parts.length > 1) {
+ String key = parts[0];
+ List<String> values = new ArrayList<>(Arrays.asList(parts).subList(1, parts.length));
+ add(key, values);
+ } else {
+ myBadRows.add(line);
+ }
  }
  }
  }
 
- private void add(String theKey, List<String> theValues) {
+ void clear() {
+ myFormalToNick.clear();
+ myNicknameToFormal.clear();
+ }
+
+ void add(String theKey, List<String> theValues) {
  myFormalToNick.put(theKey, theValues);
  for (String value : theValues) {
  myNicknameToFormal.putIfAbsent(value, new ArrayList<>());
@@ -57,14 +68,22 @@ int size() {
  return myFormalToNick.size();
  }
 
+ boolean isEmpty() {
+ return size() == 0;
+ }
+
+ List<String> getBadRows() {
+ return myBadRows;
+ }
+
  @Nonnull
- List<String> getNicknamesFromFormalName(String theName) {
+ public List<String> getNicknamesFromFormalName(String theName) {
  List<String> result = myFormalToNick.get(theName);
  return result == null ? new ArrayList<>() : result;
  }
 
  @Nonnull
- List<String> getFormalNamesFromNickname(String theNickname) {
+ public List<String> getFormalNamesFromNickname(String theNickname) {
  List<String> result = myNicknameToFormal.get(theNickname);
  return result == null ? new ArrayList<>() : result;
  }

diff --git a/...jpa/searchparam/nickname/NicknameSvc.java → ...ca/uhn/fhir/jpa/nickname/NicknameSvc.java b/...jpa/searchparam/nickname/NicknameSvc.java → ...ca/uhn/fhir/jpa/nickname/NicknameSvc.java
@@ -17,8 +17,12 @@
  * limitations under the License.
  * #L%
  */
-package ca.uhn.fhir.jpa.searchparam.nickname;
+package ca.uhn.fhir.jpa.nickname;
 
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.i18n.Msg;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.core.io.Resource;
 
@@ -32,22 +36,40 @@
 import java.util.List;
 import java.util.Set;
 
+/**
+ * Nickname service is used to load nicknames
+ * via a file that contains rows of comma separated names that are
+ * "similar" or nicknames of each other.
+ * -
+ * If no nickname resource is provided, nicknames/names.csv will be used instead.
+ * -
+ * If one is to be provided, it must be provided before nickname svc is invoked
+ */
 public class NicknameSvc {
- private final NicknameMap myNicknameMap = new NicknameMap();
+ private static final Logger ourLog = LoggerFactory.getLogger(NicknameSvc.class);
 
- public NicknameSvc() throws IOException {
- Resource nicknameCsvResource = new ClassPathResource("/nickname/names.csv");
- try (InputStream inputStream = nicknameCsvResource.getInputStream()) {
- try (Reader reader = new InputStreamReader(inputStream)) {
- myNicknameMap.load(reader);
- }
- }
+ private NicknameMap myNicknameMap;
+
+ private Resource myNicknameResource;
+
+ public NicknameSvc() {
+
+ }
+
+ public void setNicknameResource(Resource theNicknameResource) {
+ myNicknameResource = theNicknameResource;
  }
 
  public int size() {
+ ensureMapInitialized();
  return myNicknameMap.size();
  }
 
+ public List<String> getBadRows() {
+ ensureMapInitialized();
+ return myNicknameMap.getBadRows();
+ }
+
  public Collection<String> getEquivalentNames(String theName) {
  Set<String> retval = new HashSet<>(getNicknamesFromFormalName(theName));
 
@@ -64,11 +86,34 @@ public Collection<String> getEquivalentNames(String theName) {
 
  @Nonnull
  List<String> getNicknamesFromFormalName(String theName) {
+ ensureMapInitialized();
  return myNicknameMap.getNicknamesFromFormalName(theName);
  }
 
  @Nonnull
  List<String> getFormalNamesFromNickname(String theNickname) {
+ ensureMapInitialized();
  return myNicknameMap.getFormalNamesFromNickname(theNickname);
  }
+
+ private void ensureMapInitialized() {
+ if (myNicknameResource == null) {
+ myNicknameResource = new ClassPathResource("/nickname/names.csv");
+ }
+
+ if (myNicknameMap == null) {
+ myNicknameMap = new NicknameMap();
+ }
+ if (myNicknameMap.isEmpty()) {
+ try {
+ try (InputStream inputStream = myNicknameResource.getInputStream()) {
+ try (Reader reader = new InputStreamReader(inputStream)) {
+ myNicknameMap.load(reader);
+ }
+ }
+ } catch (IOException e) {
+ throw new ConfigurationException(Msg.code(2234) + "Unable to load nicknames", e);
+ }
+ }
+ }
 }
diff --git a/hapi-fhir-jpa/src/main/resources/.gitkeep b/hapi-fhir-jpa/src/main/resources/.gitkeep
diff --git a/...m/src/main/resources/nickname/License.txt → ...a/src/main/resources/nickname/License.txt b/...m/src/main/resources/nickname/License.txt → ...a/src/main/resources/nickname/License.txt
diff --git a/...ram/src/main/resources/nickname/README.md → ...jpa/src/main/resources/nickname/README.md b/...ram/src/main/resources/nickname/README.md → ...jpa/src/main/resources/nickname/README.md
diff --git a/...am/src/main/resources/nickname/README.txt → ...pa/src/main/resources/nickname/README.txt b/...am/src/main/resources/nickname/README.txt → ...pa/src/main/resources/nickname/README.txt
diff --git a/...ram/src/main/resources/nickname/names.csv → ...jpa/src/main/resources/nickname/names.csv b/...ram/src/main/resources/nickname/names.csv → ...jpa/src/main/resources/nickname/names.csv
diff --git a/hapi-fhir-jpa/src/test/java/ca/uhn/fhir/jpa/.gitkeep b/hapi-fhir-jpa/src/test/java/ca/uhn/fhir/jpa/.gitkeep
diff --git a/...searchparam/nickname/NicknameMapTest.java → ...hn/fhir/jpa/nickname/NicknameMapTest.java b/...searchparam/nickname/NicknameMapTest.java → ...hn/fhir/jpa/nickname/NicknameMapTest.java
@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.searchparam.nickname;
+package ca.uhn.fhir.jpa.nickname;
 
 import org.junit.jupiter.api.Test;
 

diff --git a/...searchparam/nickname/NicknameSvcTest.java → ...hn/fhir/jpa/nickname/NicknameSvcTest.java b/...searchparam/nickname/NicknameSvcTest.java → ...hn/fhir/jpa/nickname/NicknameSvcTest.java
@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.searchparam.nickname;
+package ca.uhn.fhir.jpa.nickname;
 
 import org.junit.jupiter.api.Test;
 

diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.7.3-SNAPSHOT</version>
+ <version>6.7.6-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
@@ -95,8 +95,8 @@
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
 import ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.provider.DiffProvider;
-import ca.uhn.fhir.jpa.provider.ProcessMessageProvider;
 import ca.uhn.fhir.jpa.provider.InstanceReindexProvider;
+import ca.uhn.fhir.jpa.provider.ProcessMessageProvider;
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
@@ -149,7 +149,6 @@
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.config.SearchParamConfig;
 import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
-import ca.uhn.fhir.jpa.searchparam.nickname.NicknameInterceptor;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamProvider;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
@@ -198,7 +197,6 @@
 import org.springframework.transaction.PlatformTransactionManager;
 
 import javax.annotation.Nullable;
-import java.io.IOException;
 import java.util.Date;
 
 @Configuration
@@ -772,12 +770,6 @@ public UnknownCodeSystemWarningValidationSupport unknownCodeSystemWarningValidat
  return new UnknownCodeSystemWarningValidationSupport(theFhirContext);
  }
 
- @Lazy
- @Bean
- public NicknameInterceptor nicknameInterceptor() throws IOException {
- return new NicknameInterceptor();
- }
-
  @Bean
  public ISynchronousSearchSvc synchronousSearchSvc() {
  return new SynchronousSearchSvcImpl();